$ SET DEFAULT [RED.NEWHEL]
$ ASSIGN NEWTEST.INP FOR011
$ ASSIGN NEWTEST.OUT FOR006
$ RUN [RED.NEWHEL]NEWHELIX
TITL  (C-G)3-T4-(C-G)3  UCLA  1D16  OCTAMER, ALT.HELIX STEPS OF HEXAMER ONLY
CELL  1., 1., 1., 90., 90., 90.
          Comments:  In this test example, the DNA hexadecamer of sequence
     C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G has been treated as a non-self-
     complementary octamer with strand sequences C-G-C-G-C-G-T-T and
     T-T-C-G-C-G-C-G, by deleting the P and two O's of P9.  This allows one
     to examine twist, roll, torsion angles and other parameters of the T's as
     well as of the Z-DNA C-G-C-G-C-G stem.  The "helix" parameters for the T's
     are wild, but are interesting.  (Deleting the two phosphates is
     accomplished, in BRKH input format, by changing the ATOM at the
     beginning of each of the three coordinate lines to anything else,
     in this case PHOS.  The BRKH input therefore ignores the three lines.)
     Only the first six base pairs of the octamer should be used to define
     the overall helix axis; the T's are not really part of the helix.  Hence
     the two HELX cards below are inactivated in favor of a HLX2 and continu-
     ation that list explicitly the numbers of C1', N1 and N9 atoms of C and G.
     For Z-DNA, the true helix repeats are between alternating C1' atoms:
     C to C and G to G, not C to following G or G to C.  (These comments are
     ignored by NEWHELIX because they are indented four or more spaces.)
BRKH
      FLGP  0
FPUN  0
PMIN  0
PMAX  0
NATM  320
BASE  8
     HELX  RC1' YC1'
     HELX  RN9 YN1
HLX2 8,49,49,90,27,68,68,109,309,268,268,227,290,249,249,208,=
    9,50,50,91,28,69,69,110,310,269,269,228,291,250,250,209
BROL
CYLN
TRNG
END
$ DEL FOR012.DAT;*, FOR015.DAT;*
$ EXIT